|
| Status |
Public on Oct 15, 2014 |
| Title |
eomesafh105_sphere_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole sphere stage embryo
|
| Organism |
Danio rerio |
| Characteristics |
genotype: eomesafh105
developmental stage: Sphere
strain: AB
|
| Growth protocol |
Embryos were grown in E3 embryo medium at 28.5 degrees celcius
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol according to manufacturers protocol and treated with Ambion TURBO Dnase.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to Zv9 release 68 using Tophat v2.0.5 using the options -p 8 -i 20 -I 380000 --coverage-search --microexon-search
Differential expression was determined using Cufflinks with options -p 4 -u
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each condition, and statistics for differential expression
|
| |
|
| Submission date |
Oct 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Christopher Nelson |
| E-mail(s) |
a.nelson.1@warwick.ac.uk
|
| Organization name |
University of Warwick
|
| Department |
School of Life Sciences
|
| Street address |
Gibbet Hill Campus
|
| City |
Coventry |
| ZIP/Postal code |
CV4 7AL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE51893 |
Identification of genes differentially expressed in MZeomesa embryos compared with wild-type |
| GSE51894 |
Smad2 and Eomesa |
|
| Relations |
| BioSample |
SAMN02389003 |
| SRA |
SRX370995 |
